Blender 2.8x Outliner - Manually Reorder Objects within Collection
As you've mentioned, uncheck 'Sort Alphabetically' first to allow manual arrangement. After doing that you should be able to reorder the layers by clicking and dragging them around.
The dark highlight over a collection indicates that you're joining your current selection to another and the dark line indicates that you're placing a collection above/below another collection. 
Holding down control while dragging a collection parents the current selection to the one you're dragging it into but still allows it to be higher up the hierachy.

Maybe this question was asked before a newer Blender release and a potential issue was resolved. (Using Blender 2.81a)